The binding sites of Sodium atom in the structure of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex With Two Trypsins (pdb code 3e8l). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3e8l structure was solved by R.BAO, C.-H.JIANG, C.W.CHI, S.X.LIN, Y.X.CHEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 30.0-2.5 | | Space group | C2221 | | a (A) | 76.634 | | b (A) | 110.863 | | c (A) | 152.991 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 90.00 | | Rfactor (%) | 19.4 | | Rfree (%) | 24.5 |
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Sodium binding site 1 out of 3 in 3e8l
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3e8l. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Pro121, A: Thr122, A: Ser123, A: Lys201, A: Gln203, A: Hoh275, A: Hoh293, | conact list:
| Atom | Atom | Distance (A) | | Na | CB A:Pro121 | 3.97 | | Na | C A:Pro121 | 3.87 | | Na | CA A:Pro121 | 3.75 | | Na | N A:Thr122 | 3.01 | | Na | CB A:Thr122 | 4.11 | | Na | CG2 A:Thr122 | 4.85 | | Na | OG1 A:Thr122 | 3.19 | | Na | C A:Thr122 | 4.00 | | Na | CA A:Thr122 | 3.86 | | Na | O A:Ser123 | 3.48 | | Na | N A:Ser123 | 3.46 | | Na | CB A:Ser123 | 4.69 | | Na | OG A:Ser123 | 3.93 | | Na | C A:Ser123 | 4.29 | | Na | CA A:Ser123 | 4.36 | | Na | CB A:Lys201 | 4.19 | | Na | CE A:Lys201 | 3.97 | | Na | CD A:Lys201 | 4.09 | | Na | CG A:Lys201 | 3.56 | | Na | NE2 A:Gln203 | 3.73 | | Na | CD A:Gln203 | 4.99 | | Na | O A:Hoh275 | 4.60 | | Na | O A:Hoh293 | 3.20 |
| interactive model:
| Sodium binding site 2 out of 3 in 3e8l
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3e8l. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: C: Thr66, C: Phe143, A: Tyr167, A: Gln170, A: Trp208, A: Ser210, C: Act181, A: Gol2, A: Hoh250, A: Hoh289, | conact list:
| Atom | Atom | Distance (A) | | Na | OG1 C:Thr66 | 4.04 | | Na | CE2 C:Phe143 | 3.77 | | Na | CD2 C:Phe143 | 4.41 | | Na | CZ C:Phe143 | 3.86 | | Na | CE1 C:Phe143 | 4.57 | | Na | CD1 A:Tyr167 | 3.92 | | Na | CE1 A:Tyr167 | 4.29 | | Na | NE2 A:Gln170 | 3.77 | | Na | OE1 A:Gln170 | 2.90 | | Na | CD A:Gln170 | 3.72 | | Na | CZ3 A:Trp208 | 4.75 | | Na | CB A:Ser210 | 4.37 | | Na | CB A:Ser210 | 4.40 | | Na | OG A:Ser210 | 3.01 | | Na | OG A:Ser210 | 4.71 | | Na | CH3 C:Act181 | 3.84 | | Na | C C:Act181 | 4.87 | | Na | O1 A:Gol2 | 4.64 | | Na | O A:Hoh250 | 3.01 | | Na | O A:Hoh289 | 2.92 |
| interactive model:
| Sodium binding site 3 out of 3 in 3e8l
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3e8l. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: C: Ala147, A: Tyr37, A: His38, A: Phe39, A: Trp136, A: Tyr146, A: Act6, A: Hoh269, | conact list:
| Atom | Atom | Distance (A) | | Na | CB C:Ala147 | 4.11 | | Na | CD1 A:Tyr37 | 4.31 | | Na | CE1 A:Tyr37 | 4.92 | | Na | O A:His38 | 2.74 | | Na | N A:His38 | 4.46 | | Na | CB A:His38 | 3.87 | | Na | C A:His38 | 3.76 | | Na | CA A:His38 | 4.27 | | Na | N A:Phe39 | 4.82 | | Na | O A:Trp136 | 4.70 | | Na | CB A:Tyr146 | 4.84 | | Na | CD1 A:Tyr146 | 3.93 | | Na | CE1 A:Tyr146 | 4.37 | | Na | CG A:Tyr146 | 4.55 | | Na | O A:Act6 | 4.01 | | Na | CH3 A:Act6 | 1.63 | | Na | C A:Act6 | 3.11 | | Na | OXT A:Act6 | 3.83 | | Na | O A:Hoh269 | 4.12 |
| interactive model:
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